This Article Full Text (PDF) Other Versions of this Article: AEM.02789-07v1 74/11/3490    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Döpfer, D. Articles by Engel, B. Search for Related Content PubMed PubMed Citation Articles by Döpfer, D. Articles by Engel, B. Agricola Articles by Döpfer, D. Articles by Engel, B.

 Previous Article  |  Next Article 

Appl. Environ. Microbiol. doi:10.1128/AEM.02789-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Assessing Genetic Heterogeneity Within Bacterial Species Isolated From Gastro-Intestinal And Environmental Samples: How Many Isolates Does It Take?

Central Veterinary Institute of Wageningen University and Research Centre, P.O.Box 65, 8200 AB Lelystad, The Netherlands; Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Quality Milk Production Services, Cornell University, Ithaca, NY 14850, USA; Institute for Epidemiology, Federal Research Institute for Animal Health, Seestr. 55, 16868 Wusterhausen, Germany

^* To whom correspondence should be addressed. Email: dorte.dopfer{at}wur.nl.

	Abstract

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination, and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analysed per sample is determined by convention, convenience, laboratory capacity or financial resources. Statistical considerations and knowledge of the heterogeneity of bacterial populations in various sources can be used to determine the number of isolates per sample that is actually needed for to address specific research questions. We present data for intestinal Escherichia coli, Listeria monocytogenes, Klebsiella pneumoniae and Streptococcus uberis from gastro-intestinal, fecal or soil samples, characterized by ribotyping, pulsed-field gel electrophoresis, and PCR-based strain typing methods. In contrast to previous studies, all calculations are performed within a single computer program, employing software that is freely available and with in-depth explanation of the choice and derivation of prior distributions. Also, some of the model assumptions are relaxed to allow for an analysis of the special case of two (groups of) strains that are observed with different probabilities. Sample size calculations, with a Bayesian method of inference, show that from 2 to 20 isolates per sample need to be characterized to detect all strains that are present in a sample with 95% certainty. Such high numbers of isolates per sample are rarely typed in real-life due to financial or logistic constraints. This implies that investigators are not gaining maximal information on strain heterogeneity and that sources and transmission pathways may go undetected.